Literature DB >> 21578205

(1H-1,3-Benzimidazole-5,6-dicarboxylic acid)(5-carboxyl-ato-1H-1,3-benzimidazole-6-carboxylic acid)silver(I) monohydrate.

Hong Zhai1.   

Abstract

The title compound, [Ag(C(9)H(5)N(2)O(4))(C(9)H(6)N(2)O(4))]·H(2)O, contains one independent Ag atom, a neutral 1H-benzimidazole-5,6-dicarboxylic acid (bdcH), its monodeprotonated form, i.e. 5-carboxyl-ato-1H-1,3-benzimidazole-6-carboxylic acid (bdc), and one solvent water mol-ecule, the latter being disordered over three sites with site occupancy factors of 0.375 (× 2) and 0.25. In addition, the H atom on one carboxylic acid residue is disordered, being connected to each of the O atoms 50% of the time. The Ag atom is in a virtually linear geometry defined by two N atoms derived from the bdc and bdcH ligands. The three-dimensional supra-molecular structure is stablized by extensive O-H⋯O and N-H⋯O hydrogen bonds. An intramolecular O-H⋯O hydrogen bond is also present.

Entities:  

Year:  2009        PMID: 21578205      PMCID: PMC2971189          DOI: 10.1107/S1600536809044535

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For related structures, see: Gao et al. (2008 ▶); Li et al. (2009 ▶); Lo et al. (2007 ▶); Wei et al. (2008 ▶); Yao et al. (2008 ▶).

Experimental

Crystal data

[Ag(C9H5N2O4)(C9H6N4O2)]·H2O M = 537.37 Monoclinic, a = 28.483 (3) Å b = 18.6398 (17) Å c = 7.2251 (7) Å β = 99.046 (1)° V = 3788.2 (6) Å3 Z = 8 Mo Kα radiation μ = 1.13 mm−1 T = 298 K 0.31 × 0.23 × 0.19 mm

Data collection

Bruker APEXII area-detector diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2004 ▶) T min = 0.740, T max = 0.807 10329 measured reflections 3675 independent reflections 2572 reflections with I > 2σ(I) R int = 0.044

Refinement

R[F 2 > 2σ(F 2)] = 0.039 wR(F 2) = 0.092 S = 1.04 3675 reflections 307 parameters 18 restraints H-atom parameters constrained Δρmax = 0.52 e Å−3 Δρmin = −0.59 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809044535/tk2558sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809044535/tk2558Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
[Ag(C9H5N2O4)(C9H6N2O4)]·H2OF(000) = 2145.0
Mr = 537.37Dx = 1.885 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2071 reflections
a = 28.483 (3) Åθ = 2.4–22.4°
b = 18.6398 (17) ŵ = 1.13 mm1
c = 7.2251 (7) ÅT = 298 K
β = 99.046 (1)°Block, colourless
V = 3788.2 (6) Å30.31 × 0.23 × 0.19 mm
Z = 8
Bruker APEXII area-detector diffractometer3675 independent reflections
Radiation source: fine-focus sealed tube2572 reflections with I > 2σ(I)
graphiteRint = 0.044
φ and ω scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)h = −35→35
Tmin = 0.740, Tmax = 0.807k = −20→22
10329 measured reflectionsl = −8→7
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.04P)2] where P = (Fo2 + 2Fc2)/3
3675 reflections(Δ/σ)max = 0.001
307 parametersΔρmax = 0.52 e Å3
18 restraintsΔρmin = −0.59 e Å3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/UeqOcc. (<1)
Ag10.374338 (11)0.168833 (16)0.58373 (5)0.04290 (14)
O10.36561 (10)−0.26003 (15)0.5821 (5)0.0606 (10)
H10.3710−0.30490.58320.073*
O20.44076 (10)−0.23159 (15)0.5698 (5)0.0547 (9)
O30.45996 (10)−0.11508 (16)0.3045 (4)0.0470 (8)
H30.4863−0.10560.26880.056*0.50
O40.50175 (10)−0.08915 (16)0.5782 (4)0.0491 (8)
H40.5006−0.08300.69400.059*0.50
O50.30757 (10)0.53188 (16)0.6824 (5)0.0548 (9)
O60.28554 (11)0.42025 (16)0.6978 (5)0.0580 (10)
O70.37366 (11)0.60136 (15)0.6187 (5)0.0538 (9)
H70.34930.57810.63860.065*
O80.44651 (11)0.58811 (16)0.5706 (5)0.0612 (10)
N10.33935 (11)0.07120 (16)0.6181 (5)0.0314 (8)
N20.28969 (11)−0.01398 (17)0.6799 (5)0.0338 (8)
H2A0.2646−0.03380.70950.041*
N30.41656 (11)0.25914 (16)0.5533 (5)0.0384 (9)
N40.47918 (11)0.32435 (17)0.5099 (5)0.0395 (9)
H4A0.50710.33470.48710.047*
C10.29744 (13)0.0560 (2)0.6672 (6)0.0354 (10)
H1A0.27570.09080.69050.043*
C20.32928 (12)−0.0490 (2)0.6369 (6)0.0287 (9)
C30.36007 (13)0.00500 (19)0.5978 (6)0.0275 (9)
C40.40427 (13)−0.01206 (19)0.5503 (6)0.0288 (9)
H4B0.42510.02370.52470.035*
C50.41601 (13)−0.0831 (2)0.5424 (6)0.0301 (9)
C60.38460 (13)−0.1378 (2)0.5819 (6)0.0293 (9)
C70.34103 (14)−0.1213 (2)0.6295 (6)0.0349 (10)
H7A0.3202−0.15690.65570.042*
C80.40022 (15)−0.2145 (2)0.5758 (6)0.0366 (10)
C90.46214 (15)−0.0985 (2)0.4738 (7)0.0392 (11)
C100.46025 (15)0.2587 (2)0.5131 (7)0.0428 (11)
H10A0.47620.21700.48950.051*
C110.44556 (13)0.3720 (2)0.5500 (6)0.0327 (10)
C120.40613 (13)0.3312 (2)0.5766 (6)0.0327 (9)
C130.36540 (13)0.3643 (2)0.6177 (6)0.0327 (10)
H13A0.33960.33670.63930.039*
C140.36314 (13)0.4380 (2)0.6266 (6)0.0321 (10)
C150.40400 (14)0.47992 (19)0.5986 (6)0.0314 (9)
C160.44451 (14)0.4463 (2)0.5622 (6)0.0352 (10)
H16A0.47110.47320.54580.042*
C170.40890 (16)0.5620 (2)0.5952 (6)0.0395 (11)
C180.31614 (14)0.4648 (2)0.6704 (6)0.0399 (11)
O1W0.2366 (4)0.1989 (7)0.851 (2)0.126 (5)0.38
H1C0.23790.20420.96810.151*0.38
H1D0.22550.15650.84230.151*0.38
O2W0.2352 (4)0.2876 (6)0.5630 (19)0.108 (4)0.38
H2C0.24950.32570.60520.129*0.38
H2D0.25300.25090.58120.129*0.38
O3W0.2637 (6)0.2800 (10)0.809 (3)0.110 (6)0.25
H3C0.27020.32230.77670.131*0.25
H3D0.25640.26470.91110.131*0.25
U11U22U33U12U13U23
Ag10.0433 (2)0.02077 (18)0.0675 (3)−0.00497 (15)0.01755 (17)0.00033 (16)
O10.0401 (18)0.0188 (16)0.126 (3)−0.0020 (13)0.0233 (19)0.0014 (17)
O20.0414 (18)0.0328 (18)0.096 (3)0.0092 (14)0.0283 (17)0.0062 (17)
O30.0345 (16)0.059 (2)0.051 (2)−0.0025 (14)0.0147 (15)−0.0074 (16)
O40.0297 (16)0.064 (2)0.054 (2)−0.0008 (15)0.0076 (15)0.0002 (16)
O50.0422 (18)0.0341 (19)0.093 (3)0.0100 (14)0.0259 (18)−0.0047 (17)
O60.0364 (17)0.0408 (19)0.104 (3)−0.0013 (15)0.0317 (18)−0.0021 (18)
O70.0478 (19)0.0226 (16)0.096 (3)0.0029 (14)0.0256 (19)0.0006 (16)
O80.049 (2)0.0314 (19)0.110 (3)−0.0119 (15)0.032 (2)−0.0032 (18)
N10.0261 (18)0.0219 (17)0.047 (2)−0.0002 (14)0.0087 (15)−0.0005 (15)
N20.0201 (16)0.033 (2)0.051 (2)−0.0036 (14)0.0140 (15)−0.0005 (16)
N30.0298 (18)0.0201 (18)0.068 (3)0.0007 (14)0.0167 (17)0.0010 (16)
N40.0279 (18)0.030 (2)0.066 (3)0.0014 (15)0.0215 (17)0.0003 (17)
C10.028 (2)0.028 (2)0.051 (3)0.0021 (18)0.008 (2)−0.0022 (19)
C20.0202 (19)0.028 (2)0.039 (3)−0.0009 (16)0.0099 (17)−0.0025 (18)
C30.0240 (19)0.022 (2)0.037 (2)−0.0045 (16)0.0071 (17)0.0005 (17)
C40.0220 (19)0.024 (2)0.042 (3)−0.0034 (16)0.0110 (18)0.0015 (17)
C50.024 (2)0.030 (2)0.037 (3)−0.0024 (17)0.0052 (17)0.0002 (18)
C60.031 (2)0.0189 (19)0.038 (3)−0.0007 (16)0.0056 (19)0.0010 (17)
C70.032 (2)0.026 (2)0.049 (3)−0.0042 (18)0.012 (2)0.0023 (19)
C80.035 (2)0.027 (2)0.052 (3)0.0037 (19)0.017 (2)−0.0011 (19)
C90.034 (2)0.029 (2)0.057 (3)0.0048 (19)0.013 (2)−0.001 (2)
C100.038 (2)0.026 (2)0.068 (3)0.0064 (19)0.018 (2)−0.001 (2)
C110.028 (2)0.025 (2)0.047 (3)−0.0020 (17)0.0123 (19)0.0020 (18)
C120.033 (2)0.022 (2)0.045 (3)0.0006 (18)0.0105 (18)0.0026 (19)
C130.028 (2)0.024 (2)0.049 (3)−0.0010 (17)0.0154 (19)0.0035 (18)
C140.028 (2)0.028 (2)0.042 (3)0.0061 (17)0.0098 (18)−0.0003 (18)
C150.033 (2)0.021 (2)0.042 (3)−0.0025 (17)0.0095 (19)0.0004 (17)
C160.029 (2)0.026 (2)0.052 (3)−0.0052 (17)0.013 (2)0.0035 (19)
C170.045 (3)0.029 (2)0.045 (3)−0.003 (2)0.011 (2)−0.001 (2)
C180.031 (2)0.035 (3)0.055 (3)0.001 (2)0.011 (2)0.000 (2)
O1W0.100 (7)0.111 (7)0.168 (9)0.017 (6)0.025 (7)−0.013 (7)
O2W0.096 (7)0.071 (6)0.158 (9)−0.017 (6)0.025 (6)0.000 (6)
O3W0.095 (9)0.102 (9)0.142 (10)−0.019 (7)0.050 (8)0.029 (8)
Ag1—N32.100 (3)C2—C31.393 (5)
Ag1—N12.108 (3)C3—C41.393 (5)
O1—C81.307 (5)C4—C51.369 (5)
O1—H10.8498C4—H4B0.9300
O2—C81.205 (5)C5—C61.415 (5)
O3—C91.254 (5)C5—C91.503 (5)
O3—H30.8499C6—C71.374 (5)
O4—C91.267 (5)C6—C81.500 (5)
O4—H40.8500C7—H7A0.9300
O5—C181.280 (5)C10—H10A0.9300
O6—C181.242 (5)C11—C161.388 (5)
O7—C171.277 (5)C11—C121.394 (5)
O7—H70.8499C12—C131.387 (5)
O8—C171.215 (5)C13—C141.378 (5)
N1—C11.329 (5)C13—H13A0.9300
N1—C31.385 (5)C14—C151.442 (5)
N2—C11.328 (5)C14—C181.508 (5)
N2—C21.380 (4)C15—C161.375 (5)
N2—H2A0.8600C15—C171.536 (5)
N3—C101.322 (5)C16—H16A0.9300
N3—C121.391 (5)O1W—H1C0.8500
N4—C101.339 (5)O1W—H1D0.8501
N4—C111.370 (5)O2W—H2C0.8501
N4—H4A0.8600O2W—H2D0.8501
C1—H1A0.9300O3W—H3C0.8496
C2—C71.391 (5)O3W—H3D0.8496
N3—Ag1—N1173.32 (12)C2—C7—H7A121.3
C8—O1—H1120.1O2—C8—O1124.2 (4)
C9—O3—H3109.5O2—C8—C6122.9 (4)
C9—O4—H4115.8O1—C8—C6112.9 (3)
C17—O7—H7114.2O3—C9—O4121.2 (4)
C1—N1—C3104.7 (3)O3—C9—C5117.2 (4)
C1—N1—Ag1132.6 (3)O4—C9—C5121.4 (4)
C3—N1—Ag1122.6 (2)N3—C10—N4113.2 (3)
C1—N2—C2107.4 (3)N3—C10—H10A123.4
C1—N2—H2A126.3N4—C10—H10A123.4
C2—N2—H2A126.3N4—C11—C16133.1 (4)
C10—N3—C12105.0 (3)N4—C11—C12106.3 (3)
C10—N3—Ag1126.3 (3)C16—C11—C12120.6 (3)
C12—N3—Ag1128.6 (2)C13—C12—N3131.1 (3)
C10—N4—C11107.0 (3)C13—C12—C11120.4 (4)
C10—N4—H4A126.5N3—C12—C11108.5 (3)
C11—N4—H4A126.5C14—C13—C12120.0 (4)
N2—C1—N1113.2 (3)C14—C13—H13A120.0
N2—C1—H1A123.4C12—C13—H13A120.0
N1—C1—H1A123.4C13—C14—C15119.3 (3)
N2—C2—C7132.6 (3)C13—C14—C18112.9 (3)
N2—C2—C3105.5 (3)C15—C14—C18127.8 (4)
C7—C2—C3121.9 (3)C16—C15—C14120.0 (4)
N1—C3—C2109.3 (3)C16—C15—C17111.7 (3)
N1—C3—C4130.2 (3)C14—C15—C17128.2 (3)
C2—C3—C4120.5 (3)C15—C16—C11119.6 (3)
C5—C4—C3117.8 (3)C15—C16—H16A120.2
C5—C4—H4B121.1C11—C16—H16A120.2
C3—C4—H4B121.1O8—C17—O7121.2 (4)
C4—C5—C6121.5 (3)O8—C17—C15119.1 (4)
C4—C5—C9115.5 (3)O7—C17—C15119.7 (4)
C6—C5—C9122.9 (3)O6—C18—O5119.8 (4)
C7—C6—C5120.9 (3)O6—C18—C14118.7 (4)
C7—C6—C8120.3 (3)O5—C18—C14121.5 (4)
C5—C6—C8118.8 (3)H1C—O1W—H1D97.8
C6—C7—C2117.3 (3)H2C—O2W—H2D112.1
C6—C7—H7A121.3H3C—O3W—H3D130.0
D—H···AD—HH···AD···AD—H···A
O1—H1···O7i0.851.772.603 (4)168
O3—H3···O3ii0.851.712.528 (5)162
O4—H4···O4iii0.851.662.500 (6)168
O7—H7···O50.851.542.389 (4)176
N2—H2A···O6iv0.861.882.733 (4)173
N4—H4A···O8v0.862.042.805 (4)148
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1⋯O7i0.851.772.603 (4)168
O3—H3⋯O3ii0.851.712.528 (5)162
O4—H4⋯O4iii0.851.662.500 (6)168
O7—H7⋯O50.851.542.389 (4)176
N2—H2A⋯O6iv0.861.882.733 (4)173
N4—H4A⋯O8v0.862.042.805 (4)148

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

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1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Poly[[(μ-1H-benzimidazole-5,6-dicarboxyl-ato)zinc(II)] monohydrate].

Authors:  Zhao-Yang Li; Jing-Wei Dai; Shan-Tang Yue
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-13

3.  Penta-aqua-(1H-benzimidazole-5,6-di-carboxyl-ato-κN)copper(II) penta-hydrate.

Authors:  Qian Gao; Wei-Hong Gao; Chao-Yan Zhang; Ya-Bo Xie
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-06-19
  3 in total
  2 in total

1.  Poly[(acetato-κO,O')aqua-(μ(4)-1H-benzimidazole-5,6-dicarboxyl-ato-κN:O,O:O,O:O)praseodymium(III)].

Authors:  Zi-Yu Pan; Jin-Hua Chen; Jian-Fen Lin; Xuan Xu; Yi-Fan Luo
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-09-25

2.  Poly[(μ-1H-benzimidazole-5,6-dicarboxyl-ato)lead(II)].

Authors:  Jinhua Chen; Chun Zheng; Yuezhu Wang; Tingting Yun; Yifan Luo
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-05-14
  2 in total

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